| anova.haplo.glm | Analysis of variance for haplo.glm model fit | 
| anova.haplo.glmlist | Analysis of variance for haplo.glm model fit | 
| chisq.power | Power and sample size for the chi-square distribution | 
| chisq.power.dif | Power and sample size for the chi-square distribution | 
| chisq.sample.size | Power and sample size for the chi-square distribution | 
| dglm.fit | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| f.power | Power and sample size for the F distribution | 
| f.power.dif | Power and sample size for the F distribution | 
| f.sample.size | Power and sample size for the F distribution | 
| find.beta.qt.phase.known | Find beta coefficients for risk haplotypes, for specified r2 | 
| find.haplo.beta.qt | Find beta coefficients for risk haplotypes, for specified r2 | 
| find.intercept.logistic | Compute either power or sample size for haplotype associations in a case-control study. | 
| find.intercept.qt.phase.known | Find beta coefficients for risk haplotypes, for specified r2 | 
| fitted.haplo.glm | Fitted values from haplo.glm fit | 
| geno.count.pairs | Counts of Total Haplotype Pairs Produced by Genotypes | 
| geno1to2 | convert genotype matrix from 1-column 2-column | 
| get.hapPair | Get a list of objects for haplotype pairs | 
| Ginv | Compute Generalized Inverse of Input Matrix | 
| haplo.binomial | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| haplo.cc | Haplotype Association Analysis in a Case-Control design | 
| haplo.chistat | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| haplo.design | Build a design matrix for haplotypes | 
| haplo.em | EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci | 
| haplo.em.control | Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci | 
| haplo.em.fitter | Compute engine for haplotype EM algorithm | 
| haplo.enum | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| haplo.glm | GLM Regression of Trait on Ambiguous Haplotypes | 
| haplo.glm.control | Create list of control parameters for haplo.glm | 
| haplo.group | Frequencies for Haplotypes by Grouping Variable | 
| haplo.hash | Integer Rank Codes for Haplotypes | 
| haplo.model.frame | Sets up a model frame for haplo.glm | 
| haplo.power.cc | Compute either power or sample size for haplotype associations in a case-control study. | 
| haplo.power.cc.ncp | Compute either power or sample size for haplotype associations in a case-control study. | 
| haplo.power.qt | Compute either power or sample size for haplotype associations with a quantitative trait. | 
| haplo.power.qt.ncp | Compute either power or sample size for haplotype associations with a quantitative trait. | 
| haplo.scan | Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window | 
| haplo.scan.obs | Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window | 
| haplo.scan.sim | Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window | 
| haplo.score | Score Statistics for Association of Traits with Haplotypes | 
| haplo.score.glm | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| haplo.score.merge | Merge haplo.score And haplo.group Objects | 
| haplo.score.podds | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| haplo.score.slide | Score Statistics for Association of Traits with Haplotypes | 
| hapPower.demo | Set of haplotypes and frequencies for power and sample size calculations | 
| hla.demo | HLA Loci and Serologic Response to Measles Vaccination | 
| locator.haplo | Find Location from Mouse Clicks and Print Haplotypes on Plot | 
| locus | Creates an object of class "locus" | 
| louis.info | Louis Information for haplo.glm | 
| mf.gindx | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| na.geno.keep | Remove rows with NA in covariates, but keep genotypes with NAs | 
| plot.haplo.score | Plot Haplotype Frequencies versus Haplotype Score Statistics | 
| plot.haplo.score.slide | Plot a haplo.score.slide Object | 
| plot.seqhap | Plot a seqhap object | 
| print.haplo.cc | Print a haplo.cc object | 
| print.haplo.em | Print contents of a haplo.em object | 
| print.haplo.glm | GLM Regression of Trait on Ambiguous Haplotypes | 
| print.haplo.group | Print a haplo.group object | 
| print.haplo.scan | Print a haplo.scan object | 
| print.haplo.score | Print a haplo.score object | 
| print.haplo.score.merge | Print a haplo.score.merge object | 
| print.haplo.score.slide | Print the contents of a haplo.score.slide object | 
| print.seqhap | Sequential Haplotype Scan Association Analysis for Case-Control Data | 
| print.summary.haplo.glm | Print and summary of a haplo.glm object | 
| printBanner | Print a nice banner | 
| residScaledGlmFit | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| residuals.haplo.glm | Accessing residuals for haplo.glm fit | 
| score.sim.control | Create the list of control parameters for simulations in haplo.score | 
| seqhap | Sequential Haplotype Scan Association Analysis for Case-Control Data | 
| seqhap.dat | Simulated data for seqhap examples | 
| seqhap.pos | Simulated data for seqhap examples | 
| setupGeno | Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class. | 
| sr.class | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| sr.class<- | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| summary.haplo.em | Summarize contents of a haplo.em object | 
| summary.haplo.glm | Print and summary of a haplo.glm object | 
| summaryGeno | Summarize Full Haplotype Enumeration on Genotype Matrix | 
| varfunc.glm.fit | Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions. | 
| vcov.haplo.glm | variance-covariance matrix of a fitted haplo.glm object | 
| x.sexcheck | consistency checks for x.linked locus |